In the Bushveld Complex of South Africa, numerous granitic and granophyric rocks termed the Lebowa Granite and Rashoop Granophyre Suites, respectively, overlie the layered ultramafic-mafic rocks of the Rustenburg Layered Suite. Despite their close spatial and temporal association, the granites and granophyres are often interpreted as being unrelated to the Rustenburg Layered Suite. This paper describes the transition from the uppermost Rustenburg Layered Suite into overlying granite and granophyre at three locations in the western (the Bierkraal drill core) and eastern (Diepkloof farm and Stoffberg town) limbs of the Bushveld Complex. In the western limb, a ~60 m thick transition zone bridges the petrological gap between the overlying Nebo Granite (Lebowa Granite Suite) and Upper Zone (Rustenburg Layered Suite). Across the transition zone, the composition of olivine changes from Fo6 to Fo1, clinopyroxene from Mg#25 to Mg#2 and plagioclase from An45 to An16. At Stoffberg in the eastern limb, the Upper Zone dioritic cumulates grade into the overlying monzonitic Roof Zone. Across the Roof Zone, plagioclase compositions change from An42 to An4, clinopyroxene from Mg#30 to Mg#11 and olivine from Fo9 to Fo5. Based on geochemistry and petrography, we correlate the lowermost stratigraphy at the farm Diepkloof with the Stoffberg Roof Zone. At Diepkloof, the Roof Zone grades into the overlying Stavoren Granophyre (Rashoop Granophyre Suite). All units are indistinguishable in terms of bulk rock Nd (εNd = −6.4 to −5.4) and Hf (εHf = −9.2 to −6.6) isotopes (corrected to 2055 Ma). Similarly, the Upper Main Zone, Upper Zone and transition zone are indistinguishable in terms of bulk rock Sr isotopes ((87Sr/86Sr)2055 Ma = 0.7071 to 0.7076, except one transition zone outlier at 0.7058). We submit that the transition zone represents the fossil record of bulk and/or diffusional mixing between coexisting Upper Zone and Nebo Granite magmas. We test this hypothesis by combining field, petrographic and geochemical observations with forward modelling using the Rhyolite-MELTS algorithm. Our work on the Bierkraal core (western limb) shows that at least a portion of the granitic magma was emplaced before the residual liquid of the Upper Zone had solidified. At Stoffberg and Diepkloof in the eastern limb (where the granite is absent), the Roof Zone underwent uninterrupted fractional crystallization.